Chapter 13:
Microbial Communities of the Male Urethra

Affiliations: 1: Division of Infectious Diseases, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294.;
2: Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202.

Traditionally, the male urethra in healthy men was believed to be sterile or only transiently colonized by microorganisms. This view reflected technical limitations in studying this site that were not easily surmounted until methods for cultivation-independent bacterial identification became available. First, while the obvious analogous compartment to the male urethra may be the female urinary tract, given the function of the penis, the male urethral compartment is most often compared to the vaginal microenvironment. A simple Gram stain of these two body sites demonstrates substantial differences. Vaginal samples from healthy women typically contain significant numbers of epithelial cells and a large number of microorganisms including Lactobacillus and Candida species among others (see chapter 12). In contrast, it is unusual to identify similar numbers of microorganisms by simple Gram stain of urethral smears obtained from healthy men. An unintended consequence has been that far less effort has gone into characterizing the relatively sparse microorganisms that are routinely observed, and ignored, in urethral specimens from healthy men. As described later in this chapter, recent cultivation-independent surveys of male urethral swab, urine, and semen specimens have confirmed that the male urethra harbors smaller absolute numbers of microorganisms than the vagina but have also identified a surprisingly diverse array of bacterial taxa, many of which correspond to pathogens and commensal organisms found in the vagina. This has led to the reemerging idea that the microbiology of the male urethra may be more complex than is appreciated and that the composition of urethral microbial communities, collectively the urethral microbiome, might play a role in male urethral health and disease analogous to the role of the vaginal microbiome.

Sequence diversity before, during, and after an STI. Total number of sequences obtained from samples collected at baseline, 1 month prior to infection with Chlamydia trachomatis, at the time infection was detected, and 1 month posttreatment.

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FIGURE 1

Sequence diversity before, during, and after an STI. Total number of sequences obtained from samples collected at baseline, 1 month prior to infection with Chlamydia trachomatis, at the time infection was detected, and 1 month posttreatment.

Exemplar timeline of community composition changes associated with STI. Example of microbial community changes associated with a common STI (C. trachomatis). The male urethral microbiome is diverse and complex prior to onset of partnered sexual behaviors. In a longitudinal study, for some men genera routinely found in the urogenital compartment are notably missing prior to and during infection with chlamydia (e.g., Acinetobacter and Propionibacterium, P values ≤ 0.05), while others (e.g., Veillonella) are first detected during chlamydial infection but remain following antibiotic treatment.

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FIGURE 2

Exemplar timeline of community composition changes associated with STI. Example of microbial community changes associated with a common STI (C. trachomatis). The male urethral microbiome is diverse and complex prior to onset of partnered sexual behaviors. In a longitudinal study, for some men genera routinely found in the urogenital compartment are notably missing prior to and during infection with chlamydia (e.g., Acinetobacter and Propionibacterium, P values ≤ 0.05), while others (e.g., Veillonella) are first detected during chlamydial infection but remain following antibiotic treatment.

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